The (re)integration of flood storage areas in the river system is considered and proved as an effective flood protection measure. By their (controlled) filling and emptying, inundation risks for downstream areas with higher vulnerability can be reduced. They have an influence not only on the flood level, but also on the residence time of the water in the river ecosystem, which is an important biological parameter. A good prediction of storage flow is therefore necessary in an integrated ecosystem model. In such a model, which is being developed by the universities of Ghent and Antwerp, hydraulic, biological and biogeochemical processes are coupled. In this paper, a one-dimensional hydrodynamic module of the integrated STRIVE (STReam RIVer Ecosystem) model, which is based on the de SaintVenant equations and solved by the Preissmann scheme, is adapted to be able to include flow exchange with storage cells. This model is validated with experimental laboratory measurements on a small scale. The flow between the storage cells and the river is controlled by weirs (flooded river banks). Model simulations with STRIVE are also compared with HEC-RAS simulations. Good agreement between simulations of both models and between the STRIVE simulations and the measurements is found.